Contacts of the helix formed by residues 189 - 198 (chain W) in PDB entry 1P7G
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 189 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186W TYR* 2.9 30.9 + - + +
187W LYS 3.1 1.1 - - - -
188W ASN* 1.3 77.8 - - - +
190W ARG* 1.3 62.3 + - - +
191W GLY* 3.3 6.2 + - - -
192W SER* 2.6 42.2 + - - -
193W TYR 3.3 7.8 + - - -
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Residues in contact with ARG 190 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178U TRP* 6.0 1.8 - - - -
133W ALA 3.3 26.9 + - - -
134W LYS* 3.7 18.3 + - - +
136W VAL* 3.0 28.9 + - - +
138W GLY* 3.2 23.6 + - - +
139W VAL* 4.9 0.4 - - - +
177W VAL* 3.7 31.0 + - + +
179W GLU* 5.3 4.2 - - - +
182W TYR* 3.1 48.5 + - + +
188W ASN 3.0 11.0 + - - +
189W ASP* 1.3 73.2 - - - +
191W GLY* 1.3 62.9 + - - +
193W TYR* 3.4 2.4 + - + +
194W VAL* 3.0 25.0 + - + +
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Residues in contact with GLY 191 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134W LYS* 3.7 25.8 - - - +
189W ASP* 3.0 6.6 + - - -
190W ARG* 1.3 79.6 - - - +
192W SER* 1.3 61.5 + - - +
194W VAL* 3.3 2.8 + - - +
195W ASP* 3.0 28.7 + - - -
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Residues in contact with SER 192 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186W TYR* 3.7 18.9 - - - -
189W ASP* 2.6 36.1 + - - -
191W GLY* 1.3 70.9 - - - +
193W TYR* 1.3 67.4 + - - +
195W ASP* 3.4 7.4 + - - +
196W ASN* 3.0 29.6 + - - +
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Residues in contact with TYR 193 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34W ILE* 4.3 23.0 - - + +
93W PHE* 3.8 15.6 - - - -
175W LEU* 3.3 25.8 - - + +
176W ASP 2.8 30.6 + - - -
177W VAL* 4.3 4.3 - - + -
181W ALA* 3.6 20.4 + - - +
182W TYR* 3.3 41.7 - + + -
186W TYR* 3.5 29.4 + + + -
189W ASP 3.3 6.8 + - - +
190W ARG* 3.5 11.7 - - + +
191W GLY 3.2 0.2 - - - -
192W SER* 1.3 79.3 - - - +
194W VAL* 1.3 75.4 + - + +
196W ASN* 3.3 2.3 + - - +
197W TRP* 3.0 23.4 + - + +
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Residues in contact with VAL 194 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130W SER* 4.1 27.4 - - - +
133W ALA* 4.1 6.7 - - + -
134W LYS* 4.1 21.5 - - + -
175W LEU* 4.0 24.9 - - + -
177W VAL* 4.1 20.0 - - + -
190W ARG* 3.0 24.8 + - + +
191W GLY 3.6 3.6 - - - +
193W TYR* 1.3 80.1 - - + +
195W ASP* 1.3 65.9 + - - +
197W TRP* 3.0 24.3 + - - +
198W TRP* 3.4 10.2 - - + +
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Residues in contact with ASP 195 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126W LYS* 5.6 0.2 + - - -
130W SER* 4.7 5.9 + - - -
134W LYS* 3.1 27.4 + - - -
191W GLY 3.0 19.5 + - - +
192W SER* 3.7 7.4 - - - +
194W VAL* 1.3 78.0 - - - +
196W ASN* 1.3 62.9 + - - +
198W TRP* 3.3 24.1 + - - +
199W ASN* 4.1 3.3 - - - +
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Residues in contact with ASN 196 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W TYR* 3.8 27.2 - - + +
186W TYR* 3.3 37.5 + - - +
192W SER* 3.0 15.3 + - - +
193W TYR 3.9 1.1 - - - +
195W ASP* 1.3 75.9 - - - +
197W TRP* 1.3 66.5 + - - +
199W ASN* 2.8 35.6 + - - +
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Residues in contact with TRP 197 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33W TYR* 5.4 1.6 - - - -
34W ILE* 4.6 7.4 - - + -
93W PHE* 4.1 3.8 - + - -
96W ASN* 5.5 0.2 - - + -
97W MSE 3.7 36.6 - - + +
129W PHE* 3.6 30.7 - + - -
173W LEU* 3.6 32.5 - - + -
174W ALA 3.6 19.1 - - - -
175W LEU* 3.4 35.8 - - + +
193W TYR* 3.0 22.4 + - + +
194W VAL* 3.0 18.3 + - - +
196W ASN* 1.3 76.5 - - - +
198W TRP* 1.3 101.1 + + - +
199W ASN 2.9 1.7 + - - -
200W VAL* 3.0 27.1 + - + +
201W VAL* 3.6 15.1 - - + +
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Residues in contact with TRP 198 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W GLY* 3.3 18.2 - - - -
105W GLY 4.2 3.6 + - - +
122W PHE* 4.4 9.2 - + - -
125W PHE* 3.7 32.1 - + - -
126W LYS* 3.6 45.1 - - + +
129W PHE* 3.8 31.2 - + + -
130W SER* 3.3 27.2 + - - -
173W LEU* 4.5 1.3 - - + -
194W VAL* 3.4 16.0 + - + +
195W ASP* 3.3 27.0 + - - +
196W ASN 3.1 1.2 + - - -
197W TRP* 1.3 93.8 - + - +
199W ASN* 1.3 61.5 + - - +
200W VAL 3.2 0.9 + - - -
201W VAL* 3.5 21.0 + - + +
203W TRP* 4.0 20.8 + + - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il